6-78885450-A-ACTTAT

Position:

• chr6-78885450-A-ACTTAT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001010844.4(IRAK1BP1):​c.381+11_381+12insTCTTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.89 (60469 hom., cov: 0)
  • Exomes 𝑓: 0.88 (482096 hom.)
• Consequence: IRAK1BP1 NM_001010844.4 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0670

Genes affected

IRAK1BP1 (HGNC:17368): (interleukin 1 receptor associated kinase 1 binding protein 1) Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-78885450-A-ACTTAT is Benign according to our data. Variant chr6-78885450-A-ACTTAT is described in ClinVar as [Benign]. Clinvar id is 2786344.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRAK1BP1	NM_001010844.4	c.381+11_381+12insTCTTA		splice_region_variant, intron_variant		ENST00000369940.7	NP_001010844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRAK1BP1	ENST00000369940.7	c.381+11_381+12insTCTTA		splice_region_variant, intron_variant		1	NM_001010844.4	ENSP00000358956	P1
IRAK1BP1	ENST00000606868.5	c.351+11_351+12insTCTTA		splice_region_variant, intron_variant, NMD_transcript_variant		1		ENSP00000475570
IRAK1BP1	ENST00000607739.1	c.120+11_120+12insTCTTA		splice_region_variant, intron_variant		2		ENSP00000475503

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135333 AN: 151620 Hom.: 60421 Cov.: 0

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.884

GnomAD3 exomes AF: 0.899 AC: 192200 AN: 213682 Hom.: 86578 AF XY: 0.899 AC XY: 105014 AN XY: 116842

Gnomad AFR exome AF: 0.890

Gnomad AMR exome AF: 0.934

Gnomad ASJ exome AF: 0.834

Gnomad EAS exome AF: 0.898

Gnomad SAS exome AF: 0.905

Gnomad FIN exome AF: 0.913

Gnomad NFE exome AF: 0.895

Gnomad OTH exome AF: 0.892

GnomAD4 exome AF: 0.881 AC: 1085213 AN: 1232048 Hom.: 482096 Cov.: 18 AF XY: 0.882 AC XY: 549102 AN XY: 622700

Gnomad4 AFR exome AF: 0.877

Gnomad4 AMR exome AF: 0.927

Gnomad4 ASJ exome AF: 0.827

Gnomad4 EAS exome AF: 0.878

Gnomad4 SAS exome AF: 0.899

Gnomad4 FIN exome AF: 0.913

Gnomad4 NFE exome AF: 0.878

Gnomad4 OTH exome AF: 0.874

GnomAD4 genome AF: 0.893 AC: 135436 AN: 151738 Hom.: 60469 Cov.: 0 AF XY: 0.894 AC XY: 66254 AN XY: 74142

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.886

Alfa AF: 0.871 Hom.: 5696

Asia WGS AF: 0.892 AC: 3090 AN: 3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4055605; hg19: chr6-79595167;